No, definite not, considering the context

My understading of the sentense is

Had the alien not left (the company), and had the alien returned under advanced parole

or
Had the alien not left under AP (AOS), and had the alien returned under advanced parole

in any way, it does not means
Had the alien not left under advanced parole , and had the alien not returned under advanced parole.

I think that first meaning is much accurate considering the context.